Contacts of the helix formed by residues 300 - 313 (chain J) in PDB entry 3Q2K
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 300 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131J GLN* 3.7 33.8 - - - +
134J ARG* 4.8 2.6 - - - +
135J ASN* 6.1 0.7 - - - -
296J VAL* 3.9 12.4 + - - -
298J GLY 3.9 0.4 - - - -
299J PHE* 1.3 75.6 - - - +
301J HIS* 1.3 67.5 + - - +
302J PRO 3.3 1.4 - - - -
303J LEU* 3.4 16.3 + - - +
304J TYR 3.4 6.2 + - - -
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Residues in contact with HIS 301 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J ILE* 4.1 9.4 - - + +
24J ASN* 3.7 27.7 + - + +
25J HIS* 3.3 37.1 + + - -
28J ALA* 3.8 16.6 - - + -
102J GLU* 2.9 20.6 + - - -
129J VAL* 4.1 6.0 - - + +
131J GLN* 3.7 30.5 + - - -
299J PHE 3.2 0.4 - - - -
300J GLY* 1.3 76.6 + - - +
302J PRO* 1.3 62.5 - - + +
304J TYR* 2.6 32.5 + + - +
305J TYR* 3.0 17.5 + + + -
500J NAI 3.8 14.4 - - - -
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Residues in contact with PRO 302 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J ASN* 5.3 1.6 - - - +
27J GLY 5.4 0.7 - - - -
28J ALA* 3.7 22.4 - - + -
31J GLN* 3.6 31.9 - - + +
32J HIS* 3.0 28.8 + - + +
299J PHE* 3.2 25.6 - - + +
300J GLY 3.4 0.4 - - - -
301J HIS* 1.3 95.1 - - + +
303J LEU* 1.3 68.1 + - + +
305J TYR 3.5 0.7 + - - +
306J ASP 3.2 6.4 + - - -
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Residues in contact with LEU 303 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J ARG* 3.7 55.4 - - + +
296J VAL* 6.0 9.0 - - + -
300J GLY* 3.4 10.1 + - - +
301J HIS 3.3 0.8 - - - -
302J PRO* 1.3 82.9 - - + +
304J TYR* 1.3 63.8 + - - +
306J ASP* 3.3 20.1 - - + +
307J ASN* 3.6 3.3 + - - +
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Residues in contact with TYR 304 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100J VAL* 4.3 7.0 - - + -
127J PHE* 3.1 25.9 - + + +
128J VAL 2.9 29.3 + - - -
129J VAL* 3.6 27.1 - - + -
130J LYS* 3.9 19.5 - - - -
131J GLN* 4.3 14.1 - - + -
134J ARG* 4.2 12.1 - - + +
300J GLY 3.4 8.5 + - - +
301J HIS* 2.6 19.3 + + - +
303J LEU* 1.3 73.6 - - - +
305J TYR* 1.3 69.1 + + - +
307J ASN* 2.9 28.7 + - + +
308J VAL* 3.2 28.4 + - + +
319J GLU* 5.7 4.3 - - + -
320J THR* 3.7 17.4 + - - -
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Residues in contact with TYR 305 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J PHE* 3.9 35.7 - + - -
25J HIS* 2.5 42.0 + + - +
28J ALA* 3.5 29.6 - - + +
29J ILE* 4.0 22.0 - - + +
32J HIS* 4.3 12.8 - - + -
77J VAL* 3.1 20.1 - - + +
100J VAL* 4.5 8.9 - - + +
301J HIS* 3.0 16.5 + + + +
302J PRO 3.5 6.3 + - - +
304J TYR* 1.3 81.8 - + - +
306J ASP* 1.3 69.9 + - - +
308J VAL* 3.0 12.4 + - + -
309J ILE* 2.7 34.5 + - + +
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Residues in contact with ASP 306 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32J HIS* 3.4 21.9 + - + -
35J ARG* 3.4 20.1 + - - -
302J PRO 3.2 7.4 + - - +
303J LEU* 3.3 16.8 - - + +
305J TYR* 1.3 77.2 - - - +
307J ASN* 1.3 57.4 + - - +
309J ILE* 3.8 2.7 - - - +
310J ASN* 2.9 51.4 + - - +
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Residues in contact with ASN 307 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J PHE* 5.0 3.3 - - - -
134J ARG* 5.5 6.5 - - - +
303J LEU 3.6 4.6 + - - +
304J TYR* 2.9 17.3 + - + +
306J ASP* 1.3 79.0 - - - +
308J VAL* 1.3 56.7 + - - +
310J ASN* 3.5 5.7 + - - +
311J CYS* 2.8 30.7 + - - +
316J CYS* 4.0 14.6 - - - +
317J GLU 3.6 20.2 + - - -
318J PRO* 3.7 3.3 - - - +
319J GLU* 2.8 40.5 + - + +
320J THR 4.6 0.2 + - - -
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Residues in contact with VAL 308 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J PHE* 3.9 30.1 - - + -
100J VAL* 4.5 8.3 - - + -
127J PHE* 3.9 34.1 - - + -
304J TYR* 3.2 38.0 + - + +
305J TYR* 3.0 14.3 + - + +
307J ASN* 1.3 75.3 - - - +
309J ILE* 1.3 54.1 + - - +
311J CYS* 2.9 3.5 + - - +
312J LEU* 2.6 49.0 + - + +
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Residues in contact with ILE 309 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J ILE* 4.8 6.1 - - + -
13J PHE* 4.2 22.2 - - + -
29J ILE* 6.0 1.3 - - - -
32J HIS* 3.6 36.1 - - + -
35J ARG* 3.6 37.2 - - + +
36J ALA* 3.7 19.5 - - + -
305J TYR* 2.7 29.2 + - + +
306J ASP 3.9 2.2 - - - +
308J VAL* 1.3 71.6 - - + +
310J ASN* 1.3 70.1 + - - +
311J CYS 2.9 1.4 + - - -
312J LEU* 3.0 6.3 + - - +
313J ARG* 2.9 34.6 + - + +
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Residues in contact with ASN 310 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J ARG* 2.8 29.7 + - - +
306J ASP* 2.9 44.3 + - - +
307J ASN* 3.9 3.9 - - - +
309J ILE* 1.3 73.0 - - - +
311J CYS* 1.3 61.4 + - - +
313J ARG* 3.4 4.1 + - - +
314J GLY 3.3 2.8 + - - -
315J ASP* 2.8 45.3 + - + +
316J CYS* 3.3 25.7 - - - -
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Residues in contact with CYS 311 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125J ARG* 3.8 28.6 + - - -
127J PHE* 3.7 27.4 - - + -
307J ASN* 2.8 15.8 + - - +
308J VAL 2.9 8.0 + - - +
310J ASN* 1.3 78.0 - - - +
312J LEU* 1.3 57.6 + - - +
314J GLY* 2.9 21.7 + - - -
316J CYS* 3.3 29.5 - - - +
317J GLU 4.5 0.4 - - - -
318J PRO* 3.7 20.0 - - + -
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Residues in contact with LEU 312 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J PRO* 3.8 5.5 - - - +
6J ILE* 3.1 26.7 + - + +
11J ILE* 4.1 30.7 - - + -
13J PHE* 4.6 0.2 - - + -
74J ASP* 5.4 1.6 - - + -
75J ALA* 3.9 28.3 - - + -
98J HIS* 3.8 39.0 - - + +
125J ARG* 4.2 7.6 - - + +
127J PHE* 3.9 23.1 - - + -
308J VAL* 2.6 35.1 + - + +
309J ILE 3.0 2.9 + - - +
311J CYS* 1.3 73.6 - - - +
313J ARG* 1.3 58.7 + - - +
314J GLY* 3.6 0.7 + - - -
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Residues in contact with ARG 313 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J PRO* 4.7 0.4 - - - +
6J ILE 3.6 20.9 - - - +
7J THR* 2.7 56.0 + - + +
9J ARG 4.6 10.9 + - - +
11J ILE* 4.6 9.2 - - + -
35J ARG* 4.0 35.0 + - - +
309J ILE* 2.9 34.3 + - + +
310J ASN* 3.8 6.3 - - - +
311J CYS 3.1 0.2 - - - -
312J LEU* 1.3 77.1 - - - +
314J GLY* 1.3 60.2 + - - +
315J ASP* 3.4 12.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il